For decades, the American Academy of Pediatrics and the U.S. Centers for Disease Control and Prevention spoke with a single voice when advising the nation’s families on when to vaccinate their children.

Since 1995, the two organizations worked together to publish a single vaccine schedule for parents and healthcare providers that clearly laid out which vaccines children should get and exactly when they should get them.

Today, that united front has fractured. This month, the Department of Health and Human Services announced drastic changes to the CDC’s vaccine schedule, slashing the number of diseases that it recommends U.S. children be routinely vaccinated against to 11 from 17. That follows the CDC’s decision last year to reverse its recommendation that all kids get the COVID-19 vaccine.

On Monday, the AAP released its own immunization guidelines, which now look very different from the federal government’s. The organization, which represents most of the nation’s primary care and specialty doctors for children, recommends that children continue to be routinely vaccinated against 18 diseases, just as the CDC did before Robert F. Kennedy Jr. took over the nation’s health agencies.

Endorsed by a dozen medical groups, the AAP schedule is far and away the preferred version for most healthcare practitioners. California’s public health department recommends that families and physicians follow the AAP schedule.

“As there is a lot of confusion going on with the constant new recommendations coming out of the federal government, it is important that we have a stable, trusted, evidence-based immunization schedule to follow and that’s the AAP schedule,” said Dr. Pia Pannaraj, a member of AAP’s infectious disease committee and professor of pediatrics at UC San Diego.

Both schedules recommend that all children be vaccinated against measles, mumps, rubella, polio, pertussis, tetanus, diphtheria, Haemophilus influenzae type B (Hib), pneumococcal disease, human papillomavirus (HPV) and varicella (better known as chickenpox).

AAP urges families to also routinely vaccinate their kids against hepatitis A and B, COVID-19, rotavirus, flu, meningococcal disease and respiratory syncytial virus (RSV).

The CDC, on the other hand, now says these shots are optional for most kids, though it still recommends them for those in certain high-risk groups.

The schedules also vary in the recommended timing of certain shots. AAP advises that children get two doses of HPV vaccine starting at ages 9 to12, while the CDC recommends one dose at age 11 or 12. The AAP advocates starting the vaccine sooner, as younger immune systems produce more antibodies. While several recent studies found that a single dose of the vaccine confers as much protection as two, there is no single-dose HPV vaccine licensed in the U.S. yet.

The pediatricians’ group also continues to recommend the long-standing practice of a single shot combining the measles, mumps and rubella (MMR) and varicella vaccines in order to limit the number of jabs children get. In September, a key CDC advisory panel stocked with hand-picked Kennedy appointees recommended that the MMR and varicella vaccines be given as separate shots, a move that confounded public health experts for its seeming lack of scientific basis.

The AAP is one of several medical groups suing HHS. The AAP’s suit describes as “arbitrary and capricious” Kennedy’s alterations to the nation’s vaccine policy, most of which have been made without the thorough scientific review that previously preceded changes.

Days before AAP released its new guidelines, it was hit with a lawsuit from Children’s Health Defense, the anti-vaccine group Kennedy founded and previously led, alleging that its vaccine guidance over the years amounted to a form of racketeering.

The CDC’s efforts to collect the data that typically inform public health policy have noticeably slowed under Kennedy’s leadership at HHS. A review published Monday found that of 82 CDC databases previously updated at least once a month, 38 had unexplained interruptions, with most of those pauses lasting six months or longer. Nearly 90% of the paused databases included vaccination information.

“The evidence is damning: The administration’s anti-vaccine stance has interrupted the reliable flow of the data we need to keep Americans safe from preventable infections,” Dr. Jeanne Marrazzo wrote in an editorial for Annals of Internal Medicine, a scientific journal. Marrazzo, an infectious disease specialist, was fired last year as head of the National Institute of Allergy and Infectious Diseases after speaking out against the administration’s public health policies.